A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/nfs/home/rsbg/01_fastq/04_emily_ebel_bulk_midgut_data_eg_RNAseq/HunterPipeline/02_Hisat2/logs
General Statistics
| Sample Name | % Aligned |
|---|---|
| HisatArrayCxt.79688-00 | 71.5% |
| HisatArrayCxt.79688-01 | 41.0% |
| HisatArrayCxt.79688-02 | 14.3% |
| HisatArrayCxt.79688-03 | 44.4% |
| HisatArrayCxt.79688-04 | 46.6% |
| HisatArrayCxt.79688-05 | 36.9% |
| HisatArrayCxt.79688-06 | 44.7% |
| HisatArrayCxt.79688-07 | 41.4% |
| HisatArrayCxt.79688-08 | 17.3% |
| HisatArrayCxt.79688-09 | 15.4% |
| HisatArrayCxt.79688-10 | 13.4% |
| HisatArrayCxt.79688-11 | 17.6% |
| HisatArrayCxt.79688-12 | 46.7% |
| HisatArrayCxt.79688-13 | 70.1% |
| HisatArrayCxt.79688-14 | 68.1% |
| HisatArrayCxt.79688-15 | 62.5% |
| HisatArrayCxt.79688-16 | 54.4% |
| HisatArrayCxt.79688-17 | 57.5% |
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.